Short answer. Yes, with limits. Article 645 of the Civil Code allows the owner of the servient estate to close or fence the land and even to build over the aqueduct — but only in a way that does not damage the aqueduct or make necessary repairs and cleaning impossible. The easement continues; only unnecessary interference is forbidden.
What the law says
The easement of aqueduct does not prevent the owner of the servient estate from closing or fencing it, or from building over the aqueduct in such manner as not to cause the latter any damage, or render necessary repairs and cleanings impossible.
Civil Code, Article 645 — The Servient Owner May Still Build. Read the full provision →
What the servient owner may still do
The existence of an aqueduct easement on your land does not strip you of your right to use and enjoy that land. Article 645 preserves three things you can still do: close the land, fence it, and build over the aqueduct. These rights survive the easement. You can erect walls, put up fencing, and construct structures over the waterway. What you cannot do is carry out those activities in a way that harms the aqueduct itself or makes it impossible to conduct the repairs and cleaning the waterway needs to function.
The limit: no damage, no obstruction of maintenance
Article 645 sets two conditions on building over the aqueduct. First, the construction must not damage the aqueduct. Cracking, crushing, blocking, or shifting the waterway would violate this. Second, necessary repairs and cleanings must remain possible. If your construction seals off the aqueduct so thoroughly that the dominant owner cannot reach it to maintain it, the construction goes too far. The easement carries with it the right to access and maintain — Article 645 does not remove that right, it only allows structures that coexist with it.
What the dominant owner retains
The owner of the dominant estate — the one who holds the aqueduct easement — retains the right to have the waterway function and be maintained. If your construction damages the channel, disrupts water flow, or prevents the dominant owner from performing needed repairs, the dominant owner can demand that you remedy the damage or modify the construction. The easement runs with the land: it does not disappear because you built something over it, and the dominant owner's rights are not waived by the fact that they allowed initial construction.
Practical steps before building
If you own land burdened by an aqueduct easement and want to fence or build over it, the prudent approach is to plan the construction carefully, consult the dominant owner, and document the existing condition of the aqueduct before work begins. A written agreement that specifies maintenance access points and the construction parameters reduces the risk of a later dispute. Proceeding without that clarity and then having the dominant owner claim damage to the waterway puts you in a difficult position — you would need to show that the damage was not caused by your work.