Ecosystems are leaky buckets, and few more so than river ecosystems. Theory suggests that downstream transport of organic matter and bi-directional movement of organisms can influence patterns aquatic productivity and stability in rivers, but quantitative evaluations have been limited. Recent advances incorporating abiotic-dependant spatial connectivity in ecosystem and food-web models provide an opportunity to investigate how connectivity influences aquatic ecosystem function (productivity) and stability (temporal variability). Here, we examine how variation in connectivity amongst sequential reaches within a modelled river network influences patterns of productivity and stability using a spatially explicit food-web model accounting for transport and movement of organic matter (periphyton) and organisms (invertebrates and fish). We simulate the effects of connectivity between reaches via incorporating: (1) downstream transport rate (decreasing retention) of periphyton and aquatic invertebrates, and (2) bi-directional movement rate of fish. We found incorporating reach-scale transport rates of periphyton and invertebrates decreased network-scale capacity to support fish consumers but also decreased variability via spatial resource asynchrony mechanisms. Introducing bi-directional connectivity increased both fish biomass and decreased variability in some circumstances but depended on the fish movement rates between reaches. These modelled findings suggest restoring both ecosystem function and stability may require a delicate balance between multiple productivity and stability mechanisms such as promoting organic matter retention (e.g., floodplain restoration), and increasing connectivity to mobile organisms (e.g., removing movement barrier).