Below there is a summary of selected extra activities in Waterfront, specifically those, which may prove a bit problematic.
1) Mobile Command Center - There are two Jammers in Waterfront district and just as in the case of other city districts it would be good to locate and destroy them before taking actions against mobile command center. Of course I advise you to be careful, as the roofs of buildings where Jammers are will be guarded by enemies with supernatural powers (you can avoid the threat by destroying the turrets over a large distance).
As for the mobile command center, it is located in the D.U.P. headquarters in the northern part of the district (a small harbor). Here, you need to take some precautions, for there is an elite soldier with a minigun in the area, as well as a couple of Auto-Turrets. I suggest you first jump on the highway extending over the base and shoot at the elite enemy and other targets from that place. As for the towers, jumping down at the lower level in the right place you will give you a convenient position behind them, so you can easily get close to the Turrets and sabotage them. Proceed to destroying the mobile command center only after thoroughly clearing the area.
2) Blast Shards - One of the hardest accessible tracker drones is on a small balcony near the enemy base at the docks (the northern part of the district), and in order to safely reach that you need to use floating ability after bouncing from the railings. If you are currently using Smoke category, Smoke Dash ability might be useful here too (Circle on the pad).
Another shard that is difficult to obtain is located on the platform above the water, as shown in the picture above. It is located in the north-western part of the Waterfront district. Start on a shelf, south of its destination. You can bounce up from the shelf (Neon category) and glide directly towards the platform with the collectible or alternatively keep using floating and Smoke Dash (Smoke category) interchangeably.
3) Hidden Camera - The camera you seek is in the place shown in the above screenshot.
4) Audio Log - Once you start searching for the audio log, you need to examine a small alley, where you will find litter bins (picture above).