Research over the past 2 decades has shown that seasonally flooded lands support a suite of native fishes and provide food web subsidies within and to downstream habitats . At the same time, these studies have shown that the Yolo Bypass is far from optimal habitat because the landscape has been altered to drain relatively quickly, and is often disconnected from the Sacramento River by levees and weirs that create major passage problems for upstream migrating adult fishes, such as Chinook Salmon and sturgeon . Several of these issues will be addressed in coming years by proposed structural changes to Fremont Weir at the upstream end of Yolo Bypass, and by the additional improvements to the floodplain’s water distribution system . However, the question remains whether changes to agricultural land management and infrastructure can provide reliable fish habitat that can increase the growth and survival of juvenile native fishes, and thereby contribute to reversing their overall decline, aid in the recovery of native fishes listed under the U.S. and California Endangered Species acts, and increase the availability of fishery resources. To help the overarching objective of providing reliable fish habitat, our team conducted a series of field studies during 2012-2017. To test fish and food web responses within different land-management scenarios, we conducted our project on standard rice and winter wheat fields, adjacent fallow lands, and rice fields with different harvest practices or other experimental modifications. This work yielded several publications that provided insight into habitat conditions in flooded rice fields for fish and invertebrates . The focus of our effort was on rearing habitat for young Chinook Salmon, but this work may also be relevant to other native fishes. The goal of this paper is to summarize the key lessons learned from 6 years of research on the feasibility of using farm fields as rearing habitat for juvenile Chinook Salmon in the Yolo Bypass and other Central Valley locations. Our hope is that our summary will provide guidance to future researchers, as well as inform managers as they evaluate potential management approaches. An important caveat is that our studies were not intended as a proof of concept for any specific management actions. Rather, our research was intended to examine some of the attributes that could reduce limitations to rearing conditions identified in early research,hydroponic grow table and gain insight into some of the key considerations for potential future agricultural floodplain management.

A second major caveat is that we had to rely on juvenile hatchery Chinook Salmon as a surrogate for wild Chinook Salmon, our ultimate target for habitat restoration. We recognize that there are several potential differences in the behavior of hatchery and wild Chinook Salmon . However, hatchery salmon were the only feasible alternative in this case since downstream migrating wild juvenile Chinook Salmon were mostly cut off from the Yolo Bypass because of extreme drought conditions. Nonetheless, hatchery salmon have been used successfully as a research tool in many types of ecological studies, so many of the lessons learned here should have at least some relevance to wild Sacramento River Chinook Salmon. Finally, our project was separate from a number of other fish management research projects in agricultural parcels, such as current efforts to investigate whether invertebrates grown on flooded rice fields can be used as a food subsidy for adjacent river channels . Previous research has shown that inundated Yolo Bypass floodplain habitat typically has substantially higher densities of phytoplankton, zooplankton, and drift invertebrates than the adjacent Sacramento River across a suite of water year types . Our studies consistently showed that managed inundation of agricultural fields supported statistically higher levels of phytoplankton and invertebrates than the Sacramento River . Also notable was that phytoplankton and zooplankton densities in our flooded experimental fields in Yolo Bypass were higher than those measured during river inundated flood events and in the Toe Drain, a perennial tidal channel . In addition, the invertebrate community in flooded rice fields was completely dominated by zooplankton , particularly Cladocera, whereas drift invertebrates such as Diptera were found in higher concentrations in study sites at Conaway Ranch and Dos Rios. Drift invertebrates are often a more substantial part of the food web in natural flood events in Yolo Bypass . Nonetheless, zooplankton densities can be relatively high in Yolo Bypass during dry seasons and drought years . The specific reasons for these differences include longer residence time and shallower depths in the Yolo Bypass than in adjacent perennial river channels.

Water source also may have been important for quantity and composition of invertebrates, including zooplankton, since all the managed flooding work was conducted using water from Knights Landing Ridge Cut, not the Sacramento River.Given the high densities of prey in the flooded fields, along with the low metabolic costs of maintaining position in a relatively low-velocity environment, it is not surprising that growth rates of juvenile salmon were comparatively high . This result was consistent across approaches used: cages, enclosures open to the substrate, and free-swimming fish. When cages were used, salmon were PIT tagged to track individual fish growth rates within a specific habitat. We consistently found that salmon growth rates in cages placed in flooded in rice fields were higher than growth rates for juvenile Chinook Salmon of comparative life stage in any of the adjacent riverine habitats and in other regions . Growth rates were also comparatively high when free-swimming salmon were introduced into larger-scale, 0.8-ha flooded agricultural fields. These studies were more representative than those using cages of how migrating salmon might use these habitats under natural flow events. For the multiple years that free-swimming salmon were used , they averaged a mean daily growth rate of 0.98mm d−1. Throughout all study years, caged salmon and free-swimming salmon showed very similar growth rates within the same experimental study units, despite the fact that they likely experienced different micro-habitat conditions . This observation suggests that our salmon growth results were not influenced by cage effects, a well-known issue in enclosure studies . To better understand managed floodplain processes across the region, in 2015, salmon were introduced in fields at a variety of locations in the Central Valley with various vegetative substrates: Sutter Bypass , three locations on the Yolo Bypass , and Dos Rios Ranch at the confluence of the Tuolumne and San Joaquin rivers . At all of the locations, juvenile Chinook Salmon grew at rates similar to those observed in experiments conducted at Knaggs Ranch in the Yolo Bypass during previous study years. These results suggest that multiple geographical regions and substrate types can support high growth rates of juvenile Chinook Salmon.

Throughout the 2012–2016 study period, we consistently observed that juvenile Chinook Salmon were attracted to sources of inflow, and that this sometimes became the dominant factor in the distribution of salmon on experimental fields or in enclosures. In the previously described PITtag observations in 2013, salmon in both enclosures positioned themselves nearest the inflow, regardless of surrounding habitat structure . This result is not surprising, given that juvenile stream salmonids commonly adopt and defend flow oriented positions in stream environments for acquisition of drifting food resources. On flooded agricultural fields, this orientation toward flow may not only be related to feeding behavior but may also serve to keep juvenile salmon in habitat areas that are hydrologically connected and have higher velocities. In fact, analyses of the environmental factors that predict movement of large groups of tagged juvenile Chinook Salmon in the Yolo Bypass found that drainage of flooded areas was a reliable predictor of fish emigration at downstream trapping stations . Although juvenile Chinook Salmon growth rates were consistently high across substrates and study years, we observed highly variable survival of salmon, and available evidence from the studies suggests that this was related, at least in part, to differences among years in drainage rates of the study fields and habitat availability on the floodplain at large. For example, survival in 2013 ranged from 0.0% to 29.3% in the replicated fields containing different agricultural substrates. This variability was likely unrelated to substrate type; instead, these low survival rates were most likely a result of very dry conditions across Yolo Bypass and the Central Valley, generally, when record drought conditions prevailed during 2012–2015, which affected water quantity and quality. In 2013, our replicated field study likely presented one of the only wetted floodplain areas for miles around, and thus presented a prime feeding opportunity for avian predators such as cormorants, herons, and egrets. However, when the same set of fields was used in 2016, survival was much higher . This was generally a wetter period, avian predation pressure was reduced, and we more efficiently opened the flash boards to facilitate faster drainage and fish emigration. Note, however, there were some differences in methodology among years, which may have contributed to survival variability. Taken together, these observations of free swimming salmon survival suggest that field drainage rate, and overall floodplain habitat availability,flood tray are important factors for improving survival in managed agricultural floodplain habitats. Our observations of juvenile salmon orientation to flow, and the importance of efficient drainage on survival, reinforce observations from natural floodplains that connectivity between perennial channel habitat and seasonal floodplain habitat is an essential attribute of river-floodplain systems . Connectivity of managed floodplain habitats to unmanaged habitats in the river and floodplain is therefore a foundational condition needed to allow volitional migration of juvenile salmon. Further research is needed to identify how to provide sufficient connectivity to maximize rearing and migration opportunities for wild Chinook Salmon.

Natural and managed floodplain habitat is subject to a variety of flow and environmental conditions. Variation in flow and temperature dictates when and where managed agricultural habitats may be accessible and suitable for rearing salmonids, with challenges during both wet and dry years, as well as during warm periods. As noted previously, survival in the replicated fields was variable but generally low. We associate these results with the effects of extreme drought conditions that prevailed during the core of our study from 2012 through 2015. Although our field studies were conducted during a time of year when wild salmon have historically used the Yolo Bypass floodplain , the extreme drought made for warm water temperatures, and resulted in our study site being one of the few inundated wetland locations in the region. As such, avian predators were attracted to the experimental fields, exacerbating salmon mortality during drainage. We observed high concentrations of cormorants, herons, and egrets on the experimental fields, and this concentration increased over the study period. As many as 51 wading birds and 23 cormorants were noted during a single survey.This situation highlights the importance of the weather dependent, regional context of environmental conditions, which govern how and when managed floodplains can be beneficial rearing habitats for juvenile salmon. Under certain circumstances, flooded fields can generate high salmon growth but in other scenarios, these habitats can provide poor environmental conditions for salmonids and/or become predation hot spots. Even during wetter conditions, we found that management of agricultural floodplain habitat was challenging. For example, we had hoped to test the idea of using rice field infrastructure to extend the duration of Yolo Bypass inundation events in an attempt to approximate the longer-duration events of more natural floodplains; that is, through flood extension. As noted by Takata et al. , use of the Yolo Bypass by wild Chinook Salmon is strongly tied to hydrology, and salmon quickly leave river-inundated floodplains once drainage begins. We therefore reasoned that flooded rice fields might provide an opportunity to extend the duration of flooding beyond the typical Yolo Bypass hydrograph. In 2015, a flood extension study was planned but not conducted because drought conditions precluded Sacramento River inflow via Fremont Weir. To test the flood extension concept in 2016, we needed substantial landowner cooperation and assistance to install draining structures that allowed maintenance of local flooding after high flow events. Even then, we found it difficult to maintain water levels and field integrity during the tests. In our case, we were fortunate to have the cooperation of willing landowners. Partnership with landowners was key, and would be critical with any future efforts to test the concept of flood extension. We also planned a similar test in 2017, but high and long-duration flood flows prevented the study from occurring.