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Eighteen groundwater well sites located in Kafr Al-Zayat (Egypt) were sampled monthly from January 2009 to November 2011 for microbial content, Mn+2, Fe+2, total dissolved solids (TDS), total hardness, NO3−, and turbidity. The data were analyzed combining the integrated use of factor and cluster analyses as well as the geostatistical semi-variogram modeling. The prime objectives were to assess the groundwater suitability for drinking, to document the factors governing the spatio-tempral variability, and to recognize distinctive groundwater quality patterns to help enable effective sustainability and proactive management of the limited resource.The groundwater microbial, Mn+2, Fe+2, TDS, and total hardness contents violated the drinking water local standards while the turbidity and the nitrate content complied with them. Factor analysis indicated that the microbial content is the most influential factor raising the variability potential followed, in decreasing order, by Mn2+, Fe2+, TDS, NO3−, turbidity, and finally the total hardness. Turbidity resulting from urban and agricultural runoff was strongly associated with most of the quality parameters. Quality parameters fluctuate sporadically without concrete pattern in space and time while their variability scores peak in November every year. Three spatially distinctive quality patterns were recognized that were consistent with and affected by the cumulative effects of the local topography, depth to water table, thickness of the silty clay (cap layer), surface water, and groundwater flow direction and hence the recharge from contaminated surface canals and agricultural drains.