Heterogeneity of lateral habitats along large rivers can enhance rates of ecological processes such as nutrient transformations and contaminant sequestration. Consequently, construction or reconnection of hydraulic retention zones such as side-arms is being widely promoted in river restoration projects, although limited information is available to quantify the benefits to water quality. We sampled natural side-arms and a reconstructed side-arm at different phases of hydrological connectivity on a large floodplain river in northern New Zealand to quantify changes to water quality within and between side-arms, and to determine changes associated with reconnection. Sampling of seven side-arm outlets during low flow indicated reduced NO3-N concentrations but elevated conductivity and total suspended sediment (TSS) compared with the river. Longitudinal changes within disconnected side-arms were most pronounced at outlet and/or mid-arm locations where total nitrogen and NO3-N declined relative to inlets, while TSS and conductivity increased. Concentrations of dissolved oxygen were also markedly reduced in side-arms during disconnection. The natural and reconstructed side-arms displayed different temporal responses to connectivity, with NH4-N and TSS in particular becoming elevated along the natural side-arm during low connectivity, while TSS declined and PO4-P increased along the reconstructed side-arm. These temporal differences were likely caused by (i) differences in side-arm age (time since formation) affecting substrate composition, riparian vegetation and hydrological pathways, and (ii) bioturbation by large benthic-feeding invasive fish which became trapped in natural side-arms during disconnection. These results suggest potential for side-arm reconstruction to influence water quality at the local scale if (i) large invasive fish that mobilise bottom sediments can be excluded at times of disconnection, and (ii) side-arms are maintained to ensure transformation and attenuation processes persist over time and continue to provide water quality benefits.