But it doesn't apply to pleasure boats, or to visiting boats, or to a number of other excluded categories listed in S124. The byelaw has to mention houseboats explicitly as, when they are moored, they don't need a licence. There may be some houseboats that would need a licence if they moved.
The latest 2017 version of the Water regulations :
The Environmental Permitting (England and Wales) Regulations 2016
UK Statutory Instruments
2016 No. 1154
Meaning of “water discharge activity”
3.—(1) A “water discharge activity” means any of the following—
(a)the discharge or entry to inland freshwaters, coastal waters or relevant territorial waters of any—
(i)poisonous, noxious or polluting matter,
(ii)waste matter, or
(iii)trade effluent or sewage effluent;
(b)the discharge from land through a pipe into the sea outside the seaward limits of relevant territorial waters of any trade effluent or sewage effluent;
(c)the removal from any part of the bottom, channel or bed of any inland freshwaters of a deposit accumulated by reason of any dam, weir or sluice holding back the waters, by causing it to be carried away in suspension in the waters, unless the activity is carried on in the exercise of a power conferred by or under any enactment relating to land drainage, flood prevention or navigation;
(d)the cutting or uprooting of a substantial amount of vegetation in any inland freshwaters or so near to any such waters that it falls into them, where it is not reasonable to take steps to remove the vegetation from these waters;
(e)an activity in respect of which a notice under paragraph 4 or 5 has been served and has taken effect.
(2) A discharge or an activity that might lead to a discharge is not a “water discharge activity”—
(a)if the discharge is made, or authorised to be made, by or under any prescribed statutory provision, or
(b)if the discharge is of trade effluent or sewage effluent from a vessel.
(3) In determining whether a discharge or an activity is a water discharge activity, no account must be taken of any radioactivity possessed by any substance or article or by any part of any premises.
If it doesn't apply to pleasure boats how come everytime I've bought an EA visitor licence the lockie has checked that I didn't have a sea toilet? I did ask the chap at Teddington once what would happen if I said I did have such a toilet and he said he would send me back downstream on the next tide.