Fouling and subsequent chemical cleaning are two important issues for sustainable operation of nanofiltration (NF) membranes in water treatment and reuse applications. Fouling strongly depends on the feed water quality, especially the nature of the foulants and ionic composition of the feed water. Consequently, appropriate selection of the chemical cleaning solutions can be seen as a critical factor for effective fouling control. In this study, membrane fouling and chemical cleaning under condition typical to that in water recycling applications were investigated. Fouling conditions were achieved over approximately 18 h with foulant cocktails containing five model foulants namely humic acids, bovine serum albumin, sodium alginate, and two silica colloids in a background electrolyte solution. These model foulants were selected to represent four distinctive modes of fouling: humic acid, protein, polysaccharide, and colloidal fouling. Three chemical cleaning solutions (alkaline solution at pH 11, sodium dodecyl sulphate (SDS), and a combination of both) were evaluated for permeate flux recovery efficiency. The results indicated that with the same mass of foulant, organic fouling was considerably more severe as compared to colloidal fouling. While organic fouling caused a considerable increase in the membrane surface hydrophobicity as indicated by contact angle measurement, hydrophobicity of silica colloidal fouled membrane remained almost the same. Furthermore, a mechanistic correlation amongst cleaning efficiency, characteristics of the model foulants, and the cleaning reagents could be established. Chemical cleaning of all organically fouled membranes by a 10 mM SDS solution particularly at pH 11 resulted in good flux recovery. However, notable flux decline after SDS cleaning of organically fouled membranes was observed indicating that SDS was effective at breaking the organic foulant—Ca2+ complex but was not able to effectively dissolve and completely remove these organic foulants. Although a lower permeate flux recovery was obtained with a caustic solution (pH 11) in the absence of SDS, the permeate flux after cleaning was stable. In contrast, the chemical cleaning solutions used in this study showed low effectiveness against colloidal fouling. It is also interesting to note that membrane fouling and chemical cleaning could permanently alter the hydrophobicity of the membrane surface.