We analyzed 15-month data on seagrass species composition, % cover, shoot density, biomass and leaf growth rates from four 50 x 50 m quadrats established along a 5-km gradient in nutrients, chlorophyll-a, and siltation in Bolinao, northwestern Philippines. The gradient results from the extensive mariculture (Chanos chanos) activities in the area, which started in the 1980’s, in addition to the upland degradation done much earlier. Results show that some definite biological responses of E. acoroides and T. hemprichii to the stressors along the low-high nutrient/siltation gradient can be summed up in the following: (1) a marked decrease in the number of seagrass species, (2) percent cover in the two species did not vary significantly with the sampling months within the 15-month period; (3) an increase in cover and shoot density in E. acoroides, but a decrease in the parameters in T. hemprichii; (3) no clear relationship between the above- and below-ground biomass ratios in E. acoroides, but an increase in the ratios in T. hemprichii; and (4) the low-to-high leaf growth rates of the two species. Based on increasing sensitivity (decreasing resistance) to a combined effect of nutrients, chlorophyll-a and siltation, we propose the following sequence of the species: Enhalus acoroides > Thalassia hemprichii >Cymodocea rotundata > Halodule uninervis > C. serrulata > Halophila ovalis > Syringodium isoetifolium. We likewise propose that changes in the biological parameters in the study be considered in the search for indicators useful for a better understanding of fish farm and siltation effects on the coastal environment.