Scarcities in freshwater supply and increasingly stringent rules on wastewater discharges have emerged as major environmental concerns for petroleum refineries. Hence, this work attempts to develop an optimisation framework for refinery water network systems design and retrofit that integrates the complementary advantageous features of water pinch analysis (WPA). The framework explicitly incorporates water minimisation strategies by first postulating a superstructure representation that embeds all feasible flowsheet alternatives for implementing water reuse, regeneration and recycle (W3R) opportunities. Subsequently, a nonlinear programming (NLP) model is formulated based on the superstructure and computational experiments on a real-world case study are conducted using the GAMS/CONOPT3 modelling language platform. Post-optimality analysis on the numerical results are performed to achieve the desired water reuse quality, hence presenting a viable framework to aid decision-making in water network systems synthesis.