The importance of top-down and bottom-up mechanisms in lentic systems has largely been explored in stable systems; however, their influence is likely to change along a habitat duration gradient. Using a case study of four intermittent ponds, we test the generality of these paradigms in systems nearing the extreme short end of this gradient. Intermittent ponds fill up with water on a seasonally predictable basis, and are considered more regulated by physicochemical constraints than by biological factors. We found that natural spatial (i.e., pond-to-pond) and temporal variations (i.e., seasonal and annual) were more important than food-web manipulations (i. e., exclusion of aerial colonization, addition of top-predators [beetle larvae and odonate nymphs], and addition versus removal of allochthonous resources [leaf litter] in field enclosures) in shaping the physicochemical environment. Spatial variation included mainly depth-related variables (e. g., conductivity and pH), whereas annual variation included variables associated with hydroperiod length and productivity (e. g., weeks after flooding, pH, nutrients, and chlorophyll-a). Seasonal variation was pronounced but lower in ponds with longer hydroperiod and in mid-season. Enhanced invertebrate predation pressure increased levels of chlorophyll-a. Exclusion of aerial colonizers increased levels of chlorophyll-a and phosphorus, and affected levels of dissolved oxygen (increasing in one pond and decreasing in another). Addition of leaf litter resulted in lower concentrations of dissolved oxygen, higher phosphorus, and lower pH. Leaf litter removal led to increased levels of dissolved oxygen, changed chlorophyll-a (increasing in one pond and decreasing in another), and higher pH (in one pond). We conclude that although pond characteristics, seasonal development, and annual differences were of greater importance than biological factors for shaping the physicochemical characteristics of these intermittent ponds, bottom-up and top-down effects were also influential.