So I really like [name]Harbor[/name] or Harbour as its spelt where I live (personally I prefer the first spelling.) I really love nature names as middle names on little boys, names that are strong, but also reflect the environment.
So what are some more water or nature names? I know Nameberry has some lists, but I prefer to hear it from you, Berries! 
I really like these as possible middle names:
Other than the ones already listed, I like:
[name]Sage[/name]
[name]Oak[/name]
[name]Pine[/name]
[name]Wolf[/name]
[name]Rowan[/name]
My favourite nature/water boys’ names are:
[name]Dylan[/name] - “son of the sea”
[name]Heath[/name]
[name]Rowan[/name]
[name]Linden[/name] - though [name]Lyndon[/name] is nice too.
[name]Rio[/name]
Sardonyx
[name]Slate[/name]
[name]Flint[/name]
[name]Onyx[/name]
Animals:
[name]Jonah[/name] - “dove”
[name]Lonan[/name] - “blackbird”
[name]Ronan[/name] - “little seal”
[name]Hart[/name]
[name]Oisin[/name] & [name]Herschel[/name] - both mean “little deer”
[name]Fox[/name]
[name]Wolf[/name]
I prefer [name]Linden[/name] too, but I was told the spelling looked too feminine. 
[name]Linden[/name] doesn’t look more feminine to me than [name]Aidan[/name] (which I like) or [name]Jaden[/name]/[name]Kaden[/name]/[name]Braeden[/name] etc. which I don’t but are certainly not eyebrow-raising on the playground these days, so personally I would just go for it if I preferred it. And honestly I don’t find y’s particularly masculinizing - [name]Reilly[/name] being more male to me than [name]Rylee[/name] or whatever.
I don’t DISLIKE [name]Lyndon[/name] but I like the direct connection to the [name]Linden[/name] tree and generally prefer that “noun names” be spelled like the correct tree/gem/season/whatever in question - like I like [name]Winter[/name] more than [name]Wynter[/name] or whatever.
[name]Lyndon[/name] has more male tradition behind it than [name]Rylee[/name] or [name]Wynter[/name], but I don’t see any reason to feel shoved away from [name]Linden[/name].
As others have mentioned [name]Rowan[/name] is a lovely nature name.
Some others are:
[name]Atlas[/name] (Greek god who held up the celestial sphere and gave his name to the [name]Atlas[/name] mountains)
[name]Forest[/name]
[name]Silvester[/name] (from the Latin [name]Silva[/name] meaning “forest or wood”)
[name]Leif[/name]/[name]Leaf[/name]
[name]Bryn[/name] (Welsh name meaning “hill”)
[name]Even[/name]/[name]Eben[/name] (Hebrew name meaning “stone”)
Titch just reminded me of [name]Silas[/name], which I also really love.
And while not keen on [name]Forrest[/name] with two r’s, I do like [name]Forest[/name].
All of the [name]Peter[/name]-related names mean stone, I believe. My favourite is [name]Piers[/name], which has an incidentally beachy sound to it as well.
I prefer [name]Ilan[/name] (Hebrew, “oak”) to [name]Eben[/name], but that’s pretty random I admit.
[name]Cove[/name], [name]Fjord[/name], [name]Beck[/name], [name]Wilder[/name], [name]Hawk[/name]
Most of these have nature based meanings:
[name]Canyon[/name]
[name]Oren[/name]
[name]Bay[/name]
[name]Beck[/name]
[name]Bourne[/name]
[name]Bradford[/name]
[name]Bradman[/name]
[name]Brosnan[/name]
[name]Burbank[/name]
[name]Cedar[/name]
[name]Holmes[/name]
[name]Hurley[/name]
[name]Irving[/name]
[name]Jorah[/name]
[name]Kallan[/name]
[name]Maxwell[/name]
[name]Murray[/name]
[name]Nile[/name]
[name]Remington[/name]
[name]Seaton[/name]
Tasman
[name]Wade[/name]
[name]Windsor[/name]
[name]Zale[/name]
[name]Adler[/name]
[name]Bentley[/name]
[name]Dresden[/name]
[name]Heath[/name]
[name]Holt[/name]
[name]Hoyt[/name]
[name]Merlin[/name]
[name]Thorne[/name]
I really like nature names for boys as well. Here are some of my favorites:
[name]Arrow[/name]
[name]Bay[/name]
[name]Bayou[/name]
[name]Fox[/name]
[name]Heath[/name]
[name]Jonah[/name]
[name]Leo[/name]
[name]Peregrine[/name]
[name]Ronan[/name]
[name]Rowan[/name]
[name]Sorrel[/name]
[name]Winter[/name]
These are all guilt pleasures:
1)[name]North[/name] or [name]Njord[/name]
2)[name]Frost[/name]
3)[name]Wolfgang[/name] nn [name]Wolf[/name]
4)[name]Rowan[/name]
It isn’t necessarily a nature name, but I personally have the idea that I’d someday like to give a baby boy the middle name of [name]Muir[/name], after [name]John[/name] [name]Muir[/name]. I also like [name]Leopold[/name], after [name]Aldo[/name] [name]Leopold[/name].
[name]Birch[/name]
[name]Briar[/name]
[name]Callum[/name]- dove
I really love [name]Frost[/name] and [name]Heath[/name]. [name]One[/name] time I met an adorable little boy named [name]Reef[/name] so that has been a gp name for me ever since. =]
Here is my list of nature/element boys names. Did not have time to sort for repeats, but wanted to share.
[name]Bren[/name]
[name]Kai[/name]
[name]Kass[/name]
Kyland
[name]Leo[/name]
[name]Rocco[/name]
[name]Stine[/name]
[name]Wesley[/name]
[name]Camdan[/name]
[name]Gavan[/name]
[name]Lachlan[/name]
[name]Lennox[/name]
[name]Todd[/name]
[name]Ash[/name]
[name]Birch[/name]
[name]Nash[/name]
[name]Silas[/name]
[name]Bodhi[/name]
[name]Channing[/name]
[name]Holden[/name]
[name]Oliver[/name]
[name]Madden[/name]
[name]Rowan[/name]
[name]Everett[/name]
[name]Marlowe[/name]
[name]Jonah[/name]
[name]Rylan[/name]
[name]Ronan[/name]
[name]Hayes[/name]
[name]Ramsay[/name]
[name]Fielding[/name]
[name]Inigo[/name]
[name]Ivo[/name]
[name]Arlo[/name]
[name]Cole[/name]
[name]Hart[/name]
[name]Lucas[/name]
[name]Luke[/name]
[name]Sparrow[/name]
[name]Sylvan[/name]
[name]Park[/name]
[name]Day[/name]
[name]Lucan[/name]
[name]Fox[/name]
[name]Todd[/name]
[name]Elm[/name]
[name]Embry[/name]
[name]Bodhi[/name]
[name]Silas[/name]
[name]Gavan[/name]
[name]Lachlan[/name]
[name]Lennox[/name]
[name]Wesley[/name]
[name]Rocco[/name]
I love [name]Harbor[/name] too!
[name]Lyndon[/name] is not a nature name to me. [name]Linden[/name] is.
Some water names:
[name]Seaton[/name]/Seton
[name]Tal[/name]
[name]Dax[/name]
[name]Calder[/name]
Lir
[name]Destin[/name]
[name]Bainbridge[/name]