Maldraxxus

If your gravestone doesn't say "Rest in Peace", you end up here.

In my search for a nice safe fishing area in Maldraxxus, I decided to compile a list of potential locations, broken down by Houses and inbetween areas, going clockwise from the Seat of the Primus. Most of the water in Maldraxxus is either black sludge, green slime, or green plague-ridden water.

Theater of Pain
There are two pools right next to the flight master here. This is the safest and most convenient location I have found to fish in Maldraxxus.
/way 49.6 54.0 Pool by the Theater of Pain

House of the Chosen
Lava is not a fishable location.

The Spearhead (black area between House of Constructs and Theater of Pain)
Water is too shallow.

House of Constructs
Safe locations:
/way 38.0 37.6 Small pool with fisherman near it - along the path between the Spearhead and the House of Constructs
/way 32.8 21.2 Large pool at north end of House of Constructs surrounded by maggots, behind Dr Hivvil's building by the kyrian corpse

Mostly safe locations:
/way 34.9 35.0 Two blood pools near road outside the House; be careful of roaming elite
/way 26.8 29.0 Small pool near Corpsecutter Moroc; hostile ooze lives in the water so be careful

Sepulcher of Knowledge (black area between House of Constructs and House of Eyes)
Most of the "river" south and east of the Sepulcher of Knowledge is fishable, but be prepared for many shallow water warnings. The areas just above and below the waterfalls are best here. The isolated pools are too shallow to fish from.

/way 46.3 24.5 Top of the large waterfall; neutral oozes nearby
/way 46.3 25.8 Bottom of the large waterfall; hostile mobs nearby, but safe at the very base of the waterfall
/way 45.6 27.8 Small waterfall, upper and lower pools; hostile mobs nearby
/way 46.0 31.6 Waterfall, lower pool; hostile mobs nearby, but safe at the very base

House of Eyes
There are a few spots right next to where the House of Eyes necropolis crashed, the area called Akarek's Tears. Most of the large pool there is fishable, but be careful of the hostiles in the area and the roaming Overseer. It is safest to fish as close to the necropolis as possible. The further you are from the necropolis, the more shallow water warnings you get.

/way 50.0 18.1 Western area of pool next to the necropolis, which is almost an alcove; fish from the east bank
/way 50.7 18.1 Central area of pool next to the necropolis; fish from the west bank
/way 52.0 17.6 Eastern area of pool next to the necropolis; fish from the east bank

Forgotten Wounds (area between House of Eyes and Theater of Pain)
Water is too shallow.

House of Rituals
No fishable areas

Rotting Mound/Glutharn's Decay (black area between House of Rituals and House of Plagues)
Most of the large pool is too shallow to fish from. The fishable areas tend to be just below or above the waterfalls, plus the isolated pool to the east.

/way 75.9 47.1 Eastern Rotting Mound, fairly isolated pool with neutral oozes around; southeast of Mor'Bitan ritual altar
/way 70.7 44.6 Northern Rotting Mound, large pool at top of north waterfall, west of Mor'Bitan ritual altar; no mobs around
/way 71.9 52.4 In east half of Glutharn's Decay, before cave hidden by waterfall with Necromantic Dissidents inside; pool below Architect Lye
/way 73.6 56.2 In east half Glutharn's Decay, top 2 pools above the platform with ritual circles on it; just make sure to back up a bit - narrow area

House of Plagues
While the small pool and stream of slime south of the flight point are deep enough to fish from, there is an elite giant that roams the area and hostile mobs all around. This spot is safe if you position carefully.

/way 58.0 76.0 Mostly safe pool; stand in the northwest corner to avoid oozes and the roaming elite

The large pool containing the ruins of the House of Plagues is entirely fishable, but you receive a negative debuff while in the area. Caustic Fog is a stackable debuff that proportionally increases nature damage taken and reduces healing received by 10% per stack. There is a maximum of 9 stacks, and it refreshes every 20 seconds. However, it does not deal damage so it is feasible to fish in this area. Also to note, hostile oozes live in the area south and east of the mostly intact, large building in the center of the pool; so I wouldn't recommend fishing back there.

/way 60.4 70.4 Ramp to go back up
/way 61.1 75.5 Ramp to go back up
/way 63.2 77.6 Ramp to go back up; hostile mobs in area

DKs: Use [spell=111673] as much as possible here.