Water storage clay pots have been recently explored as method for outdoor mosquito sampling and as novel device for administrating insect-pathogenic fungi to mosquitoes. Their suitability for indoor mosquito sampling in natural conditions is unknown. We tested clay pots as indoor resting sites alongside catches by CDC light trap in an area of low malaria endemicity in northern Tanzania. Mosquitoes were caught by clay pots although the rate of female Anopheles mosquito catches was 22.64 (95% CI 11.26–45.52) times greater for CDC light traps. The proportion of fed female Anophelines was significantly higher for clay pots compared to CDC light trap (p <0.001), indicating these methods sample different populations of mosquitoes. Although we were able to identify households with a consistently higher exposure to mosquitoes by CDC light trap, there was no apparent heterogeneity in mosquito catches by clay pots. We conclude that clay pots are not a reliable tool to sample mosquitoes in the dry season in an area of low transmission intensity with Anopheles arabiensis as principle vector.