Tungiasis is a cutaneous parasitosis caused by an embedded female sand flea. The distribution of cases can be spatially heterogeneous even in areas with similar risk profiles. This study assesses household and remotely sensed environmental factors that contribute to the geographic distribution of tungiasis cases in a rural area along the Southern Kenyan Coast. Data on household tungiasis case status, demographic and socioeconomic information, and geographic locations were recorded during regular survey activities of the Health and Demographic Surveillance System, mainly during 2011. Data were joined with other spatial data sources using latitude/longitude coordinates. Generalized additive models were used to predict and visualize spatial risks for tungiasis. The household-level prevalence of tungiasis was 3.4% (272/7925). There was a 1.1% (461/41,135) prevalence of infection among all participants. A significant spatial variability was observed in the unadjusted model (p-value < 0.001). The number of children per household, earthen floor, organic roof, elevation, aluminum content in the soil, and distance to the nearest animal reserve attenuated the odds ratios and partially explained the spatial variation of tungiasis. Spatial heterogeneity in tungiasis risk remained even after a factor adjustment. This suggests that there are possible unmeasured factors associated with the complex ecology of sand fleas that may contribute to the disease’s uneven distribution.