Aquatic ecosystems are used for extensive rice-shrimp culture where the available water alternates seasonally between fresh and saline. Poor water quality has been implicated as a risk factor for shrimp survival; however, links between shrimp, water quality and their main food source, the natural aquatic biota inhabiting these ponds, are less well understood. We examined the aquatic biota and water quality of three ponds over an entire year in the Mekong Delta, Vietnam, where the growing season for the marine shrimp Penaeus monodon has been extended into the wet season, when waters freshen. The survival (30–41%) and total areal biomass (350–531 kg ha⁻¹) of shrimp was constrained by poor water quality, with water temperatures, salinity and dissolved oxygen concentrations falling outside known optimal ranges for several weeks. Declines in dissolved oxygen concentration were matched by declines in both shrimp growth rates and lipid content, the latter being indicative of nutritional condition. Furthermore, as the dry season transitioned into the wet, shifts in the taxonomic composition of phytoplankton and zooplankton were accompanied by declines in the biomass of benthic algae, an important basal food source in these systems. Densities of the benthic invertebrates directly consumed by shrimp also varied substantially throughout the year. Overall, our findings suggest that the survival, condition and growth of shrimp in extensive rice-shrimp ecosystems will be constrained when poor water quality and alternating high and low salinity negatively affect the physiology, growth and composition of the natural aquatic biota. Changes in management practices, such as restricting shrimp inhabiting ponds to the dry season, may help to address these issues and improve the sustainable productivity and overall condition of these important aquatic ecosystems.

This data set presents a food web for the Flensburg Fjord, a brackish shallow water inlet on the Baltic Sea, between Germany and Denmark. The system has a benthic and shallow water pelagic component. This food web has two noteworthy attributes: (1) inclusion of metazoan parasites and other infectious agents and (2) inclusion of ontogenetic stages of parasites with complex life cycles. Data on the free‐living assemblages and parasitism were gathered during original field sampling and supplemented with information from additional published sources and local expert knowledge. Taxonomic resolution is generally high, although some functional or taxonomic groups (e.g., phytoplankton, macroalgae, and several groups of birds) are lumped into single nodes. Each ontogenetic stage of parasites with complex life cycles is treated separately and coded accordingly. For each node, we have included additional information such as taxonomy, life history, residency, and seasonality. Further, for each link, we define a specific interaction type. The web contains 180 nodes, 123 species/assemblages, and 1577 realized links. Of the 123 species/assemblages, 6 are basal, 70 are free‐living, and 45 are infectious. We present the data and metadata in the system‐neutral format standardized by R. F. Hechinger and colleagues, and thus we recognize variables that are not represented in our data set but may be added by further study.