Surface sediments were collected from Lake Manzala, the Mediterranean coastal wetland located to the east of the Nile Delta, Egypt, to assess the effect of drain effluent on the spatial variations of sedimentary characteristics and heavy metal pollution. Grain-size compositions, textures, and heavy metal distribution patterns in sediments are presented using GIS technique. Results of the analysis of the sediment showed a clear effect of drain effluent, with an increase in fine fractions and homogeneous suspensions in transportation mode. Lake sediments were dominated by sandy mud textures, and mode of transportation was homogeneous suspension and rolling. Spatial distribution of heavy metals (Fe, Mn, Zn, Cu, Ni, Cr, and Pb) was studied in the lake’s surficial sediments, along with their relationship to drain effluent and their contamination status in the ecological system. Heavy metal pollution status was assessed by means of accepted sediment quality guidelines and contamination assessment methods (contamination factor, contamination degree, modified contamination degree, geo-accumulation, and enrichment factor). Among the determined heavy metals, Pb had the most ecological risk. Generally, the heavy metals in the surface sediments indicated pollution risk ranging from moderate to considerable, particularly, in those sites facing drains and inlets that had the highest toxic effluent. The results were interpreted by statistical means. A cluster analysis defined areas facing drain discharge and inlets as separated groups. ANOVA indicated that most of the sedimentation and studied metals directed this clustering.