Intermittent surface connectivity can influence aquatic systems, since chemical and biotic movements are often associated with water flow. Although often referred to as fill and spill, wetlands also fill and merge. We examined the effects of these connection types on water levels, ion concentrations, and biotic communities of eight prairie pothole wetlands between 1979 and 2015. Fill and spill caused pulsed surface water connections that were limited to periods following spring snow melt. In contrast, two wetlands connected through fill and merge experienced a nearly continuous, 20-year surface water connection and had completely coincident water levels. Fill and spill led to minimal convergence in dissolved ions and macroinvertebrate composition, while these constituents converged under fill and merge. The primary factor determining differences in response was duration of the surface water connection between wetland pairs. Our findings suggest that investigations into the effects of intermittent surface water connections should not consider these connections generically, but need to address the specific types of connections. In particular, fill and spill promotes external water exports while fill and merge favors internal storage. The behaviors of such intermittent connections will likely be accentuated under a future with more frequent and severe climate extremes.