I’m not sure all of these can be pulled into actual names, but I am the editor for my church’s newsletter, and I do a children’s activity page for each month’s issue, and a couple months ago, I did a puzzle based on some of the types of flowers/trees/plants/etc. that were mentioned in the Bible:
[name_f]Almond[/name_f] blossoms (maybe not almond, but [name_f]Blossom[/name_f] could work as a MN?)
Aloe (meh, I’ve got nothing. Maybe [name_f]Alondra[/name_f]? Not really Biblical, but you could use the nn Alo for it, which sounds like Aloe!)
[name_u]Cedar[/name_u] (iffy on this as a first, but I like it for a middle!)
Crocus (MAYBE a MN?)
Crown [name_f]Daisy[/name_f] (I think [name_f]Daisy[/name_f] would be adorable! This is also known as the chrysanthemum, so maybe that, too, but it’s too much for me)
[name_f]Cypress[/name_f]
Grape vines
[name_f]Lily[/name_f] of the valley (especially meaningful as it was one of [name_m]Jesus[/name_m]’ names–maybe a name like [name_f]Shoshana[/name_f]/[name_f]Susanna[/name_f], or even a more elaborate [name_f]Lily[/name_f] variant, like [name_f]Lilia[/name_f], [name_f]Liliosa[/name_f], Lilevi, [name_f]Lilibet[/name_f], or [name_f]Liliane[/name_f]/[name_f]Liliana[/name_f]?)
Mustard Seed
[name_u]Oak[/name_u]
Palm (met a woman named [name_f]Palma[/name_f] today, maybe something along those lines? Or even [name_f]Paloma[/name_f]–doves are quite meaningful in the Bible!)
Pomegranate
[name_f]Rose[/name_f] (of [name_f]Sharon[/name_f])
Tamarisk
Thistle
Thorns
Walnut tree
Wheat
[name_f]Willow[/name_f] (even if not a FN, [name_f]Willow[/name_f] would be a really nice MN–something like [name_f]Magdalena[/name_f] [name_f]Willow[/name_f]?–although I just remembered that you wanted to use family MNs, so maybe not)
[name_u]Damaris[/name_u] (I’ve heard somewhere this means heifer, so maybe not the best animal meaning, but it’s still a pretty cool name. I think [name_f]Maris[/name_f] would be a cool nn, too?)
[name_f]Shoshana[/name_f]/[name_f]Susanna[/name_f] (“lily”)
[name_f]Deborah[/name_f] (means “bee”. the more Hebrew D’vorah/[name_f]Devorah[/name_f]/Dvorah makes it a little less dated, to me?)
[name_f]Dorcas[/name_f]/[name_f]Tabitha[/name_f] (“gazelle”)
[name_f]Esther[/name_f] (“star”. [name_f]Tess[/name_f] or Estey would be really cute nns)
[name_f]Eve[/name_f] (“life”)
[name_f]Jemima[/name_f] (“dove”)
[name_f]Keziah[/name_f] (omgoodness, [name_f]Keziah[/name_f]! [name_f]Do[/name_f] you like this at all? It’s a rare Biblical name–seemingly more along the lines of your boys’ names than the girls’ names you’re not a fan of, and it means “cassia, cinnamon”. Seems to fit your criteria precisely, but I guess it doesn’t matter if you’re not a fan. :))
[name_f]Keturah[/name_f] ([name_m]Abraham[/name_m]'s second wife, after [name_f]Sarah[/name_f] died. It means “incense”)
[name_f]Naomi[/name_f] (means “pleasantness”–not sure if that really counts, but nature is very pleasant, so I figured I’d give it a shot. 
I’m not a huge [name_f]Naomi[/name_f] fan, but I do adore the Spanish form, [name_f]Noemi[/name_f])
[name_f]Noa/name_f (“motion”)
[name_f]Peninnah[/name_f] (“precious stone”, although I’m not sure I’d use it, with how awful the character really was…)
[name_f]Phoebe[/name_f] (“bright, pure”)
[name_f]Rivka[/name_f] (Hebrew form of [name_f]Rebecca[/name_f]; possibly means “a snare”)
[name_f]Sapphira[/name_f] (“sapphire”. Again, possibly not the best namesake. Still a gorgeous name, though!)
Zeruiah (rumored to mean “balm of Yahweh”, which I think is pretty nice!)
[name_f]Zillah[/name_f] (“shade”. She was the second wife of Lamech)
Other random ideas:
[name_f]Tirzah[/name_f] (not a nature name, but it means “favorable”, and is one of the daughters of Zelophehad–if you know who he is at all! I’ve always loved the story of the daughters of Zelophehad, but it is a really obscure story, haha!)
[name_f]Anna[/name_f]-variants? (I think something like [name_f]Annabel[/name_f], [name_f]Anneliese[/name_f], [name_f]Anne[/name_f]-[name_f]Claire[/name_f], [name_f]Anouk[/name_f], etc., would be lovely, and has a subtle tie to the Bible, but much more interesting than [name_f]Anna[/name_f]!)
I think [name_f]Olive[/name_f]/[name_f]Olivet[/name_f] is really fantastic, too! I like that [name_f]Olive[/name_f] hits a couple references–from the Mt. of Olives/Mt. [name_f]Olivet[/name_f] to the story of the widow who borrowed jars from everyone she knew to sell the almost unending supply of olive oil God provided, but [name_f]Olivet[/name_f] is more unusual and spunky!
I see you already got quite a few of replies, so I’m hoping this isn’t all just repeats!
Good luck!
ETA: Also, what about the [name_u]Ariel[/name_u] family? Traditionally in Hebrew culture, [name_u]Ariel[/name_u]‘s a boys’ name, but [name_f]Arielle[/name_f] or [name_f]Ariella[/name_f] work for a girl. They all mean “lion of God”, which is very naturey, and I think I remember hearing somewhere that there’s a place in Biblical [name_m]Israel[/name_m] that was called [name_u]Ariel[/name_u], as well?
I dislike [name_f]Olivia[/name_f].