Urban water bodies are indicators of anthropogenic intrusion surfacing mutability in intrinsic homeostasis. Ecological assessment of various bio-physicochemical variables at periodic intervals is vital for eventual implementation of management and conservation practices in lakes. An inter-annual monitoring of surface-waters, surface-sediments and dominant macrophytes for standard variables at 50 sampling sites in 5 zones (10 each) of Anchar and Dal lakes is carried out to assess their spatio-temporal heterogeneity under human pressures. Temperature, pH, conductivity and ionic composition of the epilimnion show p < 0.01 and R² > 0.5. The trophic range for total-P exceeds critical eutrophic index (≤ 0.05 mgL⁻¹) but nitrate-N persists beneath it (≤ 0.5 mgL⁻¹) normally. Conductivity maintains superior solute richness though autotrophic assimilation and biocalcification episodes subsidize it towards summer. The anionic predominance of HCO3-(BIC) and Cl⁻ exist alongside cationic progression of Ca > Mg > Na > K. Lime-catchment adds to Ca ascendancy and hard-waters. Agricultural runoff links with K while Cl to faunal organic pollution. Superior nitrate concentration is accumulative of human actions (agriculture, farming, sewage, factories, etc.), spring fed lake-basin, preferential NH⁴⁺ autotrophic assimilation, geogenic N-pockets and forest surface runoff. Significant Coefficient of Determination (R²) for pH versus temperature, conductivity versus pH and temperature substantiate biological uptake and calcite co-precipitation. An equation with average worldwide stream abundance (mgL⁻¹) of recorded Ca (> 15), Mg (> 4), K (> 2.3) and Na (> 6.3) besides observed average epilimnion trace element concentration (μgL⁻¹) for As (> 2), Cd (> 1), Cr (> 1), Co (> 0.2), Cu (> 10), Fe (> 700), Pb (> 3), Mn (> 7), Ni (> 1), Se (> 0.2), Sn (> 0.1) and Zn (> 20) acclaim their anthropogenic origins. However, all priority pollutants (As, Cd, Cr, Cu, Pb, Ni and Se) continued below USEPA chronic levels. Fe and Zn exceed maximum permissible limits for irrigation. The flushing-out of harmful nutrient- and contaminant-levels due to semi-drainage hydrology recuperated the aqueous volume. Sediment assessment identifies Ca-Si domination with temporal gradients in pH, bicarbonate, conductivity, Organic Carbon (OC), Organic Matter (OM), Total Nitrogen (TN) and C/N. Almost no outliers in box-plots across the select sites suggest their tranquil nature. Element composition revealed the order of Si ˃ Ca ˃ Mg ˃ K ˃ Na ˃ P ˃ S ˃ Cl. Micro and trace element quantification denote the descending series of Fe ˃ Al ˃ Zn > Mn > Cu > Cr > Ni > Co > As > Sn > Pb > Cd while Hg and Se remained Below Detection Level (BDL). Sediment pH stayed on the basic side but slender acidic nature is noticed during late summer. Significant correlation for conductivity with OC and OM (p < 0.01) establish the latter a source for nutrient ions. Total-N is complementary to OC and OM of sediments too. Active/Passive-bioaccumulation or anoxic release from sediments tends to slight gradual decline in nutrient concentration till culmination of macrophytic growth phases. Enrichment Factor (EF), Geo-accumulation Index (Igeo) and Contamination Factor (CF) expound the contaminants to be largely anthropogenic. Integrated Pollution Index (IPI) and Pollution Load Index (PLI) catalog the lakes to have moderate metal contamination. Sediment Quality Guidelines (SQG’s) point to pollution status and associated ecological risks involved. Cr, Ni and Zn exceed SQG’s but Cd and Pb don’t transcend them. As is below Effects Range Low (ERL) and Cu lags in Probable Effect Concentration (PEC). The typical C/N < 10 infers autochthonous sediment OM with low decomposition rates. Upgraded [N]:[P] ratios parallel chronic nitrogen influx. Higher temperature and lower [N]:[P] ratio during summer develop internal loading of P. But higher Al, Ca and Fe proportions in sediments inactivate P mobilization. Curbing of external N and P loads is effective in remediation but the internal supplement compensates the loss. OM or Fe/Mn- oxide decomposition and reductive dissolution respectively separate bound trace-metals near hypolimnion-sediment overlap. Lower [Ca]:[Al] sponsor exsitu human Potentially Toxic Element (PTE) transport. Nonetheless, OM enriched sediments and calcite co-precipitation together curtails PTE mobility. Macrophytes optimize ambient water quality and sediment medium. The peak biomass (gm⁻²) values on dry weight basis are 880.2, 678.4, 182.4 and 45 for Myriophyllum aquaticum, Nelumbo nucifera, Ceratophyllum demersum and Salvinia natans respectively. Dry Weight, Productivity, Net Primary Productivity (NPP) and Specific Growth Rate institute affiliated variations but species Turn-Over is highest in case of S. natans and lowest for C. demersum. The species differ in tissue nutrient and trace element concentrations but correlate with ambient water-sediment medium. The peak nutrient uptake and bioconcentration coincide with peak biomass in summer and autumn. Bioconcentration Factor (BCF) indicates hyperaccumulation for most of the metals in case of C. demersum and S. natans. Removal Potential for different elements is divergent but the pattern is related which suggests unselective absorption. Turn-over Rates for elements closer to the reference value of 1 is significant. Bioavailability of nutrients and toxins becomes fractional conjointly by flushing hydrology, biological scavenging and biocalcification. An insitu self-reclaimed nutrient balance and eco-restoration is conceivable in the region of anthro-urban intensification by limiting human perturbations, practicing periodic dredging, sediment trapping, scaled-cum-selective deweeding and construction of vegetation buffer strips.