I always think the autumn is the best time to clean out a pond, as it would be less likely to be stressful to fish or wildlife which may be in hibernation.
this will give you a chance to clear-out any decaying leaves, which may encourage harmfull bacteria which can deplete oxygen levels to a dangerous condition.
Autumn is also a good time to fit a net over the pond to prevent any more leaves falling in.
If you are completely refilling with tap water, you could be running into problems with chemicals ie chlorine and the high amount of nutrients in it these days, you can avoid this by saving some of the old water or using water thats been standing for a few days, for the chlorine to evaporate, rain-butt water is useful too.
Ps 'pond vacs' can be hired from aquatic centres.
Good luck Tbird+