Shallow Twisty Bridges: First underwater area.
Limestone outcrop (Copper)
Galena outcrop (Lead)
Silver ore (north wall cave)
Gold ore (north wall cave)
Quartz
Ribbon plant

Arctic Kelp Forest: Shallow area with long kelp plants. Surrounds Shallow Twisty Bridges
Limestone outcrop (Copper)
Quartz
Creepvine seed cluster
Creepvine sample
Salt deposit

Arctic Kelp Caves: Caves on seafloor in Arctic Kelp Forest. Easy silver and gold ore.
Limestone outcrop (Copper)
Argentine outcrop (Silver)
Calaverite outcrop (Gold)
Crystalline sulfur
Quartz
Salt deposit
Root Pustule

Sparse Arctic: Empty feeling area with iceberg caves and Titan Holefish, around the starting area.
Limestone outcrop (Copper)
Quartz
Salt deposit

Twisty Bridges: Continuation of the starting area. Advanced diving equipment required.
Limestone outcrop (Copper)
Galena outcrop (Lead)
Argentine outcrop (Silver)
Calaverite outcrop (Gold)
Quartz
Ribbon plant
Table coral
Crystalline sulfur
Salt deposit
Ion Cube (3 pieces in Precursor ruins)

Deep Twisty Bridges: Swim down in caves of Twisty Bridges. Marked by roots on the walls.
Lithium
Diamond
Gel Sack

Thermal Spires: Area at the root of the Rocket Island. Marked by smoke and stone spires.
Galena outcrop (Lead)
Argentine outcrop (Silver)
Calaverite outcrop (Gold)
Lithium
Diamond

Delta Island: South from the starting area. Previously know as Rocket Island.
Limestone outcrop (Copper)
Calaverite outcrop (Gold) (in hidden cave behind abandoned base)
Titanium Deposit (underwater)
Crystalline sulfur

Mining Site: Abandoned mining facility beneath Delta Island.
Titanium Deposit
Gold Deposit
Ruby
Ruby Deposit
Diamond Deposit

Purple Vents: To the East from Rocket Island. Marked by purple smoke.
Quartz
Lithium
Crystalline sulfur
Salt deposit

Deep Purple Vents: Cave system in Purple Vents area. Seatruck/Prawn suit required.
Quartz
Lithium
Crystalline sulfur
Salt Deposit
Gel Sack
Ion Cube, in alien ruins

Lilypad Islands: East from the Rocket Island, giant lilypads float on the surface. Includes maze-like cave system.
Limestone outcrop (Copper)
Galena outcrop (Lead)
Calaverite outcrop (Gold)
Nickel ore
Quartz
Gel Sack

Deep Lilypad Islands: Cave system below Lilypad Island seabed.
Argentine outcrop (Silver)
Calaverite outcrop (Gold)
Uraninite Crystal
Nickel ore
Magnetite
Quartz
Quartz deposit
Ruby
Diamond
Flowering Spore
Young Cotton Anemone

Tree Spires: Below Thermal Spires, marked by tree-like spires with purple vines on them.
Titanium Deposit
Limestone outcrop (Copper)
Argentine outcrop (Silver)
Calaverite outcrop (Gold)
Copper Deposit
Uraninite Crystal
Lithium
Ruby
Quartz Deposit
Spiral Chunk (only inside Ventgarden leviathans)

Crystal Caverns: Deep biome below Deep Purple Vents and Tree Spires, marked by huge crystals.
Titanium Deposit
Limestone outcrop (Copper)
Galena outcrop (Lead)
Argentine outcrop (Silver)
Copper Deposit
Uraninite Crystal
Nickel ore
Lithium
Magnetite
Quartz
Quartz Deposit
Diamond
Kyanite
Ribbon Plant

Fabricator Caverns: Further down from Crystal Caverns, marked by red cube-shaped crystals.
Titanium Deposit
Limestone outcrop (Copper)
Argentine outcrop (Silver)
Copper Deposit
Nickel Ore
Quartz
Quartz Deposit
Lithium
Ribbon Plant

Glacial Basin: Above water area in the west side of the map. Includes a forest area and multiple caves.
Titanium
Limestone outcrop (Copper)
Magnetite, in caves and spy pengling areas
Quartz
Ion Cube, in alien ruins

Arctic Spires: Area beyond the bridge in Glacial Basin. Marked by spike-shaped ice formations and round tunnels.
Titanium Deposit
Limestone outcrop (Copper)
Copper Deposit
Silver ore
Lithium
Quartz
Ion Cube, in alien ruins and spy pengling areas
Ion Cube Deposi, in alien ruins

Argentine outcrop (Silver)
Arctic Kelp Caves
Twisty Bridges
Thermal Spires
Lilypad Island Cave
Tree Spires
Crystal Caves
Fabricator Caves
Thermal Spires
Deep Lilypad Islands
Tree Spires
Crystal Caverns
Fabricator Caverns

Calaverite outcrop (Gold)
Arctic Kelp Caves
Twisty Bridges
Thermal Spires
Delta Island (in hidden cave behind abandoned base)
Lilypad Islands
Deep Lilypad Islands
Tree Spires

Copper Deposit
Tree Spires
Crystal Caverns
Fabricator Caverns
Arctic Spires

Copper ore
Glacial Basin
Arctic Spires

Creepvine sample
Arctic Kelp Forest

Creepvine seed cluster
Arctic Kelp Forest

Crystalline sulfur
Arctic Kelp Caves
Twisty Bridges
Delta Island
Purple Vents
Deep Purple Vents

Deep lily pad mushroom
Deep Lilypad Islands

Diamond
Deep Twisty Bridges
Deep Lilypad Islands
Thermal Spires
Crystal Caverns

Diamond Deposit
Mining Site

Flowering Spore
Deep Lilypad Islands

Galena outcrop (Lead)
Shallow Twisty Bridges
Twisty Bridges
Thermal Spires
Lilypad Islands
Crystal Caverns

Gel Sack
Deep Twisty Bridges
Deep Purple Vents
Lilypad Islands

Gold Ore
Shallow Twisty Bridges

Gold Deposit
Mining Site

Ion Cube (found in alien ruins)
Twisty Bridges
Deep Purple Vents
Arctic Spires

Ion Cube Deposit (found in alien ruins)
Arctic Spires

Limestone outcrop (Copper)
Shallow Twisty Bridges
Arctic Kelp Forest
Arctic Kelp Caves
Sparse Arctic
Twisty Bridges
Delta Island
Lilypad Islands
Tree Spires
Crystal Caverns
Fabricator Caverns
Glacial Basin
Arctic Spires

Lithium
Deep Twisty Bridges
Thermal Spires
Purple Vents
Deep Purple Vents
Tree Spires
Crystal Caverns
Fabricator Caverns
Arctic Spires

Magnetite
Deep Lilypad Islands
Glacial Basin, in caves and spy pengling areas
Crystal Caverns

Nickel Ore
Deep Lilypad Islands
Crystal Caverns
Fabricator Caverns

Quartz
Shallow Twisty Bridges
Arctic Kelp Forest
Arctic Kelp Caves
Sparse Arctic
Twisty Bridges
Purple Vents
Deep Purple Vents
Lilypad Islands
Deep Lilypad Islands
Crystal Caverns
Fabricator Caverns
Glacial Basin
Arctic Spires

Quartz Deposit
Tree Spires
Deep Lilypad Islands
Crystal Caverns
Fabricator Caverns

Ribbon Plant
Shallow Twisty Bridges
Twisty Bridges
Crystal Caverns
Fabricator Caverns

Root Pustule
Arctic Kelp Caves

Ruby
Mining Site
Deep Lilypad Islands
Tree Spires

Ruby Deposit
Mining Site

Salt Deposit
Arctic Kelp Forest
Arctic Kelp Caves
Sparse Arctic
Twisty Bridges
Purple Vents
Deep Purple Vents

Silver ore
Shallow Twisty Bridges
Glacial Basin
Arctic Spires

Spiral Chunk
Tree Spires (only inside Ventgarden leviathans)

Table coral
Twisty Bridges

Titanium (both ore and deposit listed here + all outcrops have a chance of Titanium)
Delta Island (underwater)
Mining Site
Tree Spires
Crystal Caverns
Fabricator Caverns
Glacial Basin
Arctic Spires

Uraninite Crystal
Deep Lilypad Islands
Tree Spires
Crystal Caverns

Young Cotton Anemone
Deep Lilypad Islands

Outcrops:

You can scan all four outcrop types and after scanning you can hover your cursor on an outcrop to see a text that tells what materials you can get from it.



Limestone Outcrop:
Copper Ore
Titanium

Galena outcrop (previously Lead outcrop):
Lead
Titanium

Argentine outcrop (previously Silver Outcrop):
Silver
Titanium

Calaverite outcrop (previously Gold Outcrop):
Gold
Titanium



Large Material Deposits:

Large Material Deposits give a great amount of one resource. They can be harvested with Prawn Suit Drill Arm. Deposits are useful in mid to late game if you want to build a large base in deep biomes and they reduce backtracking to shallow biomes. Deposits can be found on the seafloor and in above water areas they are in cave walls.

Here's the list of the materials that have a Large Deposit:
Titanium, Copper, Gold, Quartz, Ruby, Diamond, Ion Cube