Poly (N- isopropyl acrylamide) (PNIPAM) is a temperature sensitive hydrogel, with a lower critical solution temperature (LCST) between 305 – 307K, across which it exhibits a volume change from a swollen state (< 305K) to a collapsed state (>307K). The temperature at which this volume transition occurs, as well as the degree and dynamics of swelling, can be altered by changing the method of synthesis, the functionality of the crosslinker used, the temperature of synthesis as well as by the co-monomer used. However, the link between specific molecular (microscopic) and macroscopic properties is still not clearly understood. As an attempt to provide this connection, we have utilised molecular simulation techniques, including specially developed Monte Carlo (MC) and molecular dynamics (MD), to study the effect of using three different crosslinkers, namely N, N-methylene bisacrylamide (BIS) (tetra-functional), ethylene glycol dimethacrylate (EGDMA) (tetra functional) and glyoxal bis(diallylacetal) (GLY) (octa-functional) on hydrogel behaviour. The effect of these crosslinkers on hydrogel properties were monitored using local structural analysis, as well as dynamical properties, including water diffusion coefficients, hydrogen bonding lifetimes and energies, as well as the transport behaviour of selected probe molecules, including 5-fluoro-1H-pyrimidine-2,4-dione (used in the treatment of certain types of cancer). Insights are provided regarding the a-priori design of these materials for specific functions, including drug delivery applications.