The Philippine freshwater system, particularly the groundwaters, is less explored resulting to under-representation in the scientific publication. Given the continuous inadequate understanding of the groundwater ecosystem, this study focuses primarily on the impact of agricultural activities on the assemblage of groundwater biota. Sampling was done using a 37μm plankton net from dug wells and springs of agricultural and forested areas in Cebu, Philippines and stygofauna was identified to the lowest possible taxa. Principal component analysis was used to determine the relationship between the environmental parameters and species richness. Out of the 14 morphotaxa, belonging to 11 families under 9 orders found, 12 morphotaxa were observed from the agricultural sites. Some of the organisms collected can be found both in groundwater and surface waters. Ostracods (Order Podocopida) and copepods (Order Cyclopoida) showed the highest taxonomic abundance. Assessment of groundwater biota in various land uses is recommended because the habitat type influenced groundwater biota.