Unconfined and perched aquifers in irrigation commands are more prone to water logging and salinity problems. More often mathematical solutions to these complexities involved merely the source/sink terms, because the phenomena was interpreted as caused by excessive irrigation water application. Contrarily, there were many instances, where such conditions were generated out of topography, clogging of pores and dissolution of nutrients/fertilisers. Modelling analyses to such realisations are illusive in the literature. In the present paper, calibrated groundwater models in regional, perched and solute transport scales are applied to examine these issues, using multiple software MODFLOW and SWIFT. Model results conclude for exercising abrupt changes in hydraulic gradient, temporal variation of skin hydraulic conductivity and dissolution constant as the controlling factors for water-logging and salinity.