Nautical Metaphors

Taken aback, on a sailing vessel the sails were 'taken aback' when the wind was unintentionally blowing on the wrong side of the sails causing a potentially dangerous situation. Later used to indicate a difficult or unexpected situation.
Batten down the hatches, to secure the hatch covers against ingress of water in preparation for a storm or other rough conditions.
Clear the decks to get everything out of the way as a warship went into action.
Show someone the ropes to show or explain to someone how to do a task or operation. Taken from the use of ropes to orient and adjust the sails, and that each rope is belayed at a specific place.
Sail close to the wind is to operate hazardously on very slim margins, usually applied in a financial sense. Derived from the practice of sailing close to the direction of the oncoming wind, where a small shift in the wrong direction could set the vessel aback.
Loaded to the gunwales
Back and fill
On one's beam ends
Awash
Adrift
A wide berth
Flagship
Unmoored
Nail one's colors to the mast, to commit completely to a course of action, as striking the colors is no longer an option
Flying the flag
Plain sailing
With flying colors - the colors was the national flag flown at sea during battle, a ship would surrender by lowering the colors and the term is now used to indicate a triumphant victory or win.
In the doldrums
All hands to the pumps
Weathering a storm
A different tack
Swinging the lead is to avoid duty by feigning illness or injury, original a confusion between Swing the leg which related to the way dogs can run on three legs to gain sympathy and the sailor's term heaving the lead which was to take soundings.[2]
Left high and dry
Three sheets to the wind, meaning "staggering drunk," refers to a ship whose sheets have come loose, causing the sails to flap uncontrolled and the ship to meander at the mercy of the elements. Also, "Three sheets in the wind, unsteady from drink."
Sun over the yardarm: This phrase is widely used, both afloat and ashore, to indicate that the time of day has been reached at which it is acceptable to have lunch or (more commonly) to have an alcoholic beverage.
Take soundings: In suspected shallow waters, a crew member may have the task of repeatedly throwing into the water a lead line, or piece of lead tied to a string knotted every fathom, for the purpose of estimating the depth of the sea.[4] This saying the nautical equivalent of "Take the lay of the land": see how things are going, or see what people think about a proposed course of action.
By and large comes from a term for sailing a ship slightly off of the wind.
To the bitter end may have originally referred to a rope fastened to the bitt, a post attached on the deck of a ship, although this etymology has been disputed.