The daggerblade grass shrimp Palaemon pugio can be a host for many types of parasites including the microphallid trematode Microphallus turgidus and the haplosporidian hyperparasite Urosporidium crescens. Parasitic infection by trematodes can influence grass shrimp behaviors and may alter habitat selection. We conducted monthly sampling to determine the abundance, density, intensity, and prevalence of M. turgidus and U. crescens at two sites near Savannah, Georgia. The goals of this study were to determine which microhabitat type P. pugio frequented more often, either sandy substrates or rocks with the invasive and habitat altering red alga Agarophyton vermiculophyllum, which was present seasonally, and whether trematode infection corresponded to microhabitat usage. Additionally, we aimed to determine whether temporal changes in parasitic infection correlated to abiotic factors. The results indicated grass shrimp were more likely to be located over sand substrate, even when A. vermiculophyllum was present. Furthermore, the surveys did not detect a relationship between shrimp microhabitat usage and trematode abundance, density, or intensity. All analyzed measures of trematode and hyperparasite infection differed significantly among months with some instances of intraseasonal variation. A negative relationship was detected between salinity and trematode prevalence and mean abundance, but not with temperature. No relationship was observed between salinity or temperature and hyperparasite prevalence or mean abundance. Through consistent monthly sampling of a heterogeneous habitat containing a habitat-altering invasive species, this study supports previous findings that salinity plays a role in M. turgidus abundance within P. pugio and demonstrates that A. vermiculophyllum does not appear to influence host microhabitat preferences, regardless of trematode infection. However, salinity alone cannot account for all observed parasite patterns; thus, it is likely that a combination of fluctuating abiotic conditions, unaccounted for aspects of habitat structure, and the presence of other host species determines grass shrimp risk of parasite infection.