All over the world freshwater ecosystems like ponds, ditches and lakes suffer from nutrient-driven regime shifts from submerged plants to dominance by algae or free-floating plants. Although freshwaters are often connected and part of a network, most of our current knowledge on regime shifts comes from studies of isolated ecosystems. The few studies that have assessed the spatial manifestation of regime shifts overlooked the hydrological fact that the water flow through connected waters typically increases in the downstream direction. Here, we use a complex ecosystem model to show that this increase in flow does not lead to spatial differences in ecosystem state. We support these findings with a simple, analytically tractable, nutrient retention model on connected waterbodies. The model shows that all bodies have the same nutrient concentration despite spatial gradients in the flow of water as well as nutrients carried by the water. As a consequence, each connected waterbody is equally vulnerable to a regime shift, implying a regime shift to be system-wide. Furthermore, it appeared that each connected waterbody behaves the same as an isolated waterbody, implying that the vast body of theory on isolated systems, like alternative stable states theory, can still be useful for connected systems. Although these findings are violated when there is heterogeneity in lateral runoff or waterbody characteristics—leading to spatial differences in ecosystem state and therefore to differences in the vulnerability to a regime shift—they show that the typical downstream build-up of water flow does not necessarily lead to differences in ecological state, and thereby provide a basic concept to better understand the ecology of connected freshwaters.