In contradiction to the exclusion hypothesis, our previous research suggests that nematode populations grow in water-filled pores that appear smaller than their body diameter when visualizing pore structures as an array of cylindrical pores of varying diameters. Observations maybe realigned with theory using a description of structure that depicts a network of pores in which small and large pores are inter-connected allowing aquatic soil fauna to reside in large pores that remain water-filled but become hydrologically isolated during drying. This conceptualization concurs with mobile-immobile water models which attempt to understand the role of aggregates in the transport of pollutants and the concept of microhabitats which links aggregates to microfaunal habitat. To understand the relationship between pore spaces and nematode activity, in particular the effects of hydrologic isolation on net mineralization rates, a grid- based autonomous agent model was constructed where grid space represents soil structure and water distribution and nematodes are treated as individual agents, making it possible to distinguish outcomes by specific nematode behaviors regarding temperature and soil moisture status. A link between behavior and moisture was suggested by findings of previous research where very slender nematodes were growing in very moist soils whereas larger ones in drier soils. This is counter to typical theory that states nematodes are best suited to living in water-filled pores of their own diameter. The agent-based model has been compared to a cohort-based model and found to respond similarly. Current work focuses on optimizing the code and parameterizing the model to the research site and the bacterivorous nematodes on that site. Preliminary studies with a Cephalobid and Rhabditid nematode isolated from the site suggest that optimal growth temperatures are below 20C and that the nematodes may be active during mild winters.