Deep-sea sponges inhabit multiple areas of the deep North Atlantic at depths below 250 m. Living in the deep ocean, where environmental properties below the permanent thermocline generally change slowly, they may not easily acclimatize to abrupt changes in the environment. Until now consistent monitoring timeseries of the environment at deep sea sponge habitats are missing. Therefore, long-term simulation with coupled bio-physical models can shed light on the changes in environmental conditions sponges are exposed to. To investigate the variability of North Atlantic sponge habitats for the past half century, the deep-sea conditions have been simulated with a 67-year model hindcast from 1948 to 2014. The hindcast was generated using the ocean general circulation model HYCOM, coupled to the biogeochemical model ECOSMO. The model was validated at known sponge habitats with available observations of hydrography and nutrients from the deep ocean to evaluate the biases, errors, and drift in the model. Knowing the biases and uncertainties we proceed to study the longer-term (monthly to multi-decadal) environmental variability at selected sponge habitats in the North Atlantic and Arctic Ocean. On these timescales, these deep sponge habitats generally exhibit small variability in the water-mass properties. Three of the sponge habitats, the Flemish Cap, East Greenland Shelf and North Norwegian Shelf, had fluctuations of temperature and salinity in 4–6 year periods that indicate the dominance of different water masses during these periods. The fourth sponge habitat, the Reykjanes Ridge, showed a gradual warming of about 0.4°C over the simulation period. The flux of organic matter to the sea floor had a large interannual variability, that, compared to the 67-year mean, was larger than the variability of primary production in the surface waters. Lateral circulation is therefore likely an important control mechanism for the influx of organic material to the sponge habitats. Simulated oxygen varies interannually by less than 1.5 ml/l and none of the sponge habitats studied had oxygen concentrations below hypoxic levels. The present study establishes a baseline for the recent past deep conditions that future changes in deep sea conditions from observations and climate models can be evaluated against.