Halifax Harbour is one of the world's largest natural harbours and has significant environmental and economic value. A good understanding of oceanographic processes is required for pollution control and sustainable development of the Harbour. A five-level nested-grid coastal ocean circulation model known as the Nested-grid Coastal Ocean Prediction System for Halifax Harbour (NCOPS-HFX) is used to reconstruct the three-dimensional circulation and hydrography and associated temporal and spatial variability of the Harbour. The NCOPS-HFX is driven by tides, meteorological forcing, and buoyancy forcing associated with river and sewage discharges. Model performances are assessed by comparing model results with available observations including sea level from tide gauges, CTD observations, current meter records and monthly mean climatology of temperature and salinity. Model results are also used to examine the main physical processes affecting circulation and hydrography in the Harbour. It is found that the near-surface currents in the Harbour are significantly affected by tides and wind forcing with an intense tidal jet in the Narrows and a salinity front in the upper layer of Bedford Basin. The time-mean circulation produced by the model is characterized by a typical two-layer estuarine circulation with seaward flow in the upper layer and landward flow in the lower layer. The model also reproduces reasonably well the seasonal changes of temperature and salinity in the Harbour. Dispersion and retention in the Harbour are studied based on numerical passive tracer and particle tracking experiments. The e-folding flushing time is about 40 and 90 days in the upper and entire Bedford Basin respectively, 2-5 days over the Inner and Outer Harbour, and about 1 day in the Narrows.

The analyses of benthonic foraminifera in surface sediments for two-years (Oct. 2007-August 2009) and cores from Halifax Harbour (HH) were essential for short-term monitoring, and reference environment reconstruction for the remediation that started in 2008. The distribution of foraminifera in the surface sediments indicates a lateral environmental variation and positive correlation to the pollution rate in HH as the environmental purity increases seawards. The treated area, Inner Harbour, recorded a rapid environmental recovery during treatment period (2008), and reverted to its former characteristics after treatment stopped (early 2009). This recovery represented by an increase in both diversity (from <12 to >20 species) and abundance (from 120–880 to 1350-1750 individuals). Additionally, the assemblage during that period witnessed a decrease in opportunistic species (<50%), shell deformities (<11%), and inner linings (17%), and a significant increase in calcareous species. The assemblage in pre-impact environment, as inferred from cores, has a high diversity (>30 species) and abundance (>4000 individuals), a dominant calcareous record (>60%), and lower deformities (3-4%). The gradual environmental degradation due to organic enrichment in the harbour caused an increasing foraminiferal decimation to reach dramatic levels with the huge growth of Halifax city since late 1950s. This decimation led to dominance of opportunistic species (e.g., agglutinated forms such as Eggerella advena, and Reophax scottii), abundance of shell deformities, and complete absence of calcareous tests, leaving only their inner linings. Analysis of benthonic foraminifera in two cores from Sydney Harbour (SH) helped to compare contamination types in both areas (domestic in HH vs. industrial in SH). The domestic pollution in HH developed an agglutinated assemblage with low diversity, low abundance, and high ratios of inner linings. In SH the assemblage showed higher diversity (>22 species) and abundance (>4000 individuals), dominant calcareous record (>50%), and low inner linings (<10%) together with some species that had never been observed in such cold waters in Nova Scotia (Ammonia beccarii).