Your appliances brand and model numbers would be very helpful, simply because different types of appliances have various requirements. Local code requirements may vary between jurisdictions as well and you should verify whatever is below with your building department.
You’ll need the manuals for your water heater and a furnace to find out required by the manufacturer clearances for their front, rear and sides. If you don’t have them, just open the manufacturer’s website and look for installation manuals.
Everything above is under the assumption that at least one of your appliances is non-direct vent, which means that it is using combustion air for gas burning process from within your basement. If both of the appliances are direct vent type (combustion air supply from exterior / they might be 2 pipe or single pipe – double wall design) the only thing you have to worry about is clearances required by the manufacturer.
If you have more questions, please read both articles (links above) first and provide detailed information about the appliances.