Land use land cover within a watershed influences stream water quality, habitat quality, and biological community structure. As development and associated impervious surface increases in a watershed, changes in storm water and nutrient inputs generally cause declines in habitat conditions and biodiversity. The first goal of our study was to evaluate the water quality in the Charles River watershed, in which our objective (G1O1) was to establish ten 100-meter reach-scale sampling stations and conduct physical, chemical, and biological assessments. The second goal of this study was to better understand the direct and indirect effects of hierarchical variables on water quality in the Charles River watershed. Our first objective of our second goal (G2O1) was to calculate land use land cover percentages at the pour-point subwatershed and local 100-meter buffer scale for each of our ten 100-meter reach sampling stations. Our second objective of our second goal (G2O2) was to use path analysis to determine the direct and indirect effects of land use land cover and impervious surface on water quality in the Charles River watershed. The results of G1O1 were that habitat quality assessments ranged from “marginal” to “optimal” and biological quality assessments ranged from “fair” to “good“, indicating overall “fair” or better water quality conditions in the watershed. The results of G2O2 were that our path analysis resulted in differences in effects of development between the buffer and sub-watershed scale. At the buffer scale, water quality was influenced more negatively by the percentage of developed land area versus the percentage of impervious cover. While both buffer development and habitat quality had a direct effect on Streamside Biosurvey Macroinvertebrates, buffer development also directly hindered habitat quality, thus having an indirect effect on Streamside Biosurvey Macroinvertebrates through habitat. Streamside Biosurvey Macroinvertebrate scores were shown to be more sensitive to development within the buffer versus at the sub-watershed scale, where impervious cover was a more important indicator of stream water quality. Through this small case study of 10 stations within the Charles River watershed, we illustrated how citizen-science level water quality assessments can be combined with water chemistry and hierarchical LULC data to provide insights into potential direct and indirect effects on water quality. As the fields of landscape ecology and conservation continue to grow, so does our ability to determine changes in land development and devise management strategies aimed at improving water quality.