In the Mediterranean region, aquatic and riparian habitats are considered amongst the most important for bat survival. These habitats are transient in the Maltese Islands and detailed research on how different bat species cope in these conditions has not been conducted. This paper presents results on the activity of pipistrelle bats across different habitats and seasons using acoustic methods to investigate their foraging habitats in the Maltese landscapes. Regression tree analysis was used to assess the effects of several environmental variables — including climatic conditions, vegetation characteristics, and prey abundance — on foraging activity. Echolocation recordings from pipistrelle bats were obtained during 220 hours of active monitoring between summer 2012 and spring 2013. During each sampling period, a maximum of 36 sites were visited (summer, n = 36; autumn: n = 33; spring: n = 35). Agricultural landscapes, cliffs, shrublands, urban areas, woodland patches, and valleys were all represented by these study sites. Detailed analyses of echolocation calls revealed the presence of two pipistrelle species, Pipistrellus pipistrellus and P. kuhlii. The former was more frequently encountered, comprising 55% of the total echolocation recordings. Pipistrellus kuhlii showed significant seasonality in foraging activity overall (Kruskal-Wallis H(2) = 13.83, P < 0.01) and within each habitat (all P-values < 0.01). Pipistrellus pipistrellus showed seasonality over agricultural land (ANOVA F_{2, 14} = 4.13, P < 0.05). Differential habitat use by these two species during summer was revealed where P. pipistrellus showed higher activity levels over agricultural sites, while P. kuhlii showed higher activity over woodland patches. Regression tree analyses indicate insect abundance, maximum temperature, and minimum distance to an urban area to affect foraging activity of P. kuhlii, while minimum wind speed, minimum distance to an urban area, and average canopy height were found to affect the foraging activity of P. pipistrellus. Both species were found to cope with conditions found in the Maltese Islands by using an optimal foraging scheme, wherein they seasonally alternate between selective and opportunistic foraging strategies.